Starting phenix.real_space_refine on Fri Aug 22 23:36:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8id4_35357/08_2025/8id4_35357.cif Found real_map, /net/cci-nas-00/data/ceres_data/8id4_35357/08_2025/8id4_35357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8id4_35357/08_2025/8id4_35357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8id4_35357/08_2025/8id4_35357.map" model { file = "/net/cci-nas-00/data/ceres_data/8id4_35357/08_2025/8id4_35357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8id4_35357/08_2025/8id4_35357.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5545 2.51 5 N 1472 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8665 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2174 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 4 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 1, 'TRP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1761 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2572 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "Y" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 404 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "S" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1733 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'EIC': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 1.86, per 1000 atoms: 0.21 Number of scatterers: 8665 At special positions: 0 Unit cell: (106.47, 127.764, 113.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1590 8.00 N 1472 7.00 C 5545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 340.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 35.9% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 38 through 69 removed outlier: 3.619A pdb=" N ARG R 67 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 90 removed outlier: 3.635A pdb=" N LEU R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE R 82 " --> pdb=" O VAL R 78 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 101 removed outlier: 4.018A pdb=" N VAL R 95 " --> pdb=" O ALA R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 112 removed outlier: 3.691A pdb=" N HIS R 112 " --> pdb=" O VAL R 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 109 through 112' Processing helix chain 'R' and resid 113 through 142 Processing helix chain 'R' and resid 152 through 171 Processing helix chain 'R' and resid 172 through 174 No H-bonds generated for 'chain 'R' and resid 172 through 174' Processing helix chain 'R' and resid 201 through 216 removed outlier: 3.662A pdb=" N SER R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TRP R 207 " --> pdb=" O GLY R 203 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR R 213 " --> pdb=" O VAL R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 244 removed outlier: 3.663A pdb=" N THR R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL R 243 " --> pdb=" O LYS R 239 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER R 244 " --> pdb=" O ARG R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 294 removed outlier: 3.864A pdb=" N SER R 256 " --> pdb=" O GLN R 252 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG R 261 " --> pdb=" O GLN R 257 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER R 278 " --> pdb=" O PHE R 274 " (cutoff:3.500A) Proline residue: R 279 - end of helix removed outlier: 3.849A pdb=" N PHE R 292 " --> pdb=" O LEU R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 321 removed outlier: 3.867A pdb=" N TRP R 305 " --> pdb=" O SER R 301 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.546A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.681A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.198A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.613A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.655A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.938A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.546A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.636A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'R' and resid 177 through 181 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.093A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.638A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.850A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.754A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.516A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.937A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.534A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.557A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.692A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 142 removed outlier: 3.522A pdb=" N ALA S 212 " --> pdb=" O SER S 209 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 147 through 149 removed outlier: 3.792A pdb=" N GLU S 247 " --> pdb=" O VAL S 148 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU S 179 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU S 188 " --> pdb=" O LEU S 179 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2378 1.33 - 1.45: 1616 1.45 - 1.57: 4759 1.57 - 1.70: 2 1.70 - 1.82: 83 Bond restraints: 8838 Sorted by residual: bond pdb=" N THR A 327 " pdb=" CA THR A 327 " ideal model delta sigma weight residual 1.457 1.529 -0.072 1.29e-02 6.01e+03 3.12e+01 bond pdb=" CA PHE R 88 " pdb=" C PHE R 88 " ideal model delta sigma weight residual 1.524 1.584 -0.061 1.27e-02 6.20e+03 2.28e+01 bond pdb=" N ALA A 326 " pdb=" CA ALA A 326 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.20e-02 6.94e+03 1.55e+01 bond pdb=" N ILE R 89 " pdb=" CA ILE R 89 " ideal model delta sigma weight residual 1.459 1.509 -0.050 1.34e-02 5.57e+03 1.42e+01 bond pdb=" CA ALA A 326 " pdb=" C ALA A 326 " ideal model delta sigma weight residual 1.524 1.560 -0.037 1.23e-02 6.61e+03 8.84e+00 ... (remaining 8833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 11810 2.46 - 4.92: 147 4.92 - 7.38: 31 7.38 - 9.84: 2 9.84 - 12.29: 2 Bond angle restraints: 11992 Sorted by residual: angle pdb=" N ALA A 326 " pdb=" CA ALA A 326 " pdb=" C ALA A 326 " ideal model delta sigma weight residual 108.38 120.67 -12.29 1.35e+00 5.49e-01 8.29e+01 angle pdb=" N SER R 244 " pdb=" CA SER R 244 " pdb=" C SER R 244 " ideal model delta sigma weight residual 110.28 100.09 10.19 1.48e+00 4.57e-01 4.74e+01 angle pdb=" N ARG R 69 " pdb=" CA ARG R 69 " pdb=" C ARG R 69 " ideal model delta sigma weight residual 112.90 106.20 6.70 1.31e+00 5.83e-01 2.62e+01 angle pdb=" N SER R 90 " pdb=" CA SER R 90 " pdb=" C SER R 90 " ideal model delta sigma weight residual 112.34 105.71 6.63 1.30e+00 5.92e-01 2.60e+01 angle pdb=" N ILE R 89 " pdb=" CA ILE R 89 " pdb=" C ILE R 89 " ideal model delta sigma weight residual 111.44 117.93 -6.49 1.34e+00 5.57e-01 2.34e+01 ... (remaining 11987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 4753 16.82 - 33.64: 377 33.64 - 50.46: 68 50.46 - 67.29: 10 67.29 - 84.11: 9 Dihedral angle restraints: 5217 sinusoidal: 1934 harmonic: 3283 Sorted by residual: dihedral pdb=" C THR A 327 " pdb=" N THR A 327 " pdb=" CA THR A 327 " pdb=" CB THR A 327 " ideal model delta harmonic sigma weight residual -122.00 -145.78 23.78 0 2.50e+00 1.60e-01 9.05e+01 dihedral pdb=" N THR A 327 " pdb=" C THR A 327 " pdb=" CA THR A 327 " pdb=" CB THR A 327 " ideal model delta harmonic sigma weight residual 123.40 145.69 -22.29 0 2.50e+00 1.60e-01 7.95e+01 dihedral pdb=" CA ILE R 298 " pdb=" C ILE R 298 " pdb=" N TRP R 299 " pdb=" CA TRP R 299 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 5214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.171: 1391 0.171 - 0.342: 8 0.342 - 0.514: 0 0.514 - 0.685: 0 0.685 - 0.856: 1 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CA THR A 327 " pdb=" N THR A 327 " pdb=" C THR A 327 " pdb=" CB THR A 327 " both_signs ideal model delta sigma weight residual False 2.53 1.67 0.86 2.00e-01 2.50e+01 1.83e+01 chirality pdb=" CB ILE R 197 " pdb=" CA ILE R 197 " pdb=" CG1 ILE R 197 " pdb=" CG2 ILE R 197 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA SER R 244 " pdb=" N SER R 244 " pdb=" C SER R 244 " pdb=" CB SER R 244 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1397 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 171 " 0.052 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO R 172 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO R 172 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 172 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 324 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.70e+00 pdb=" C THR A 324 " -0.054 2.00e-02 2.50e+03 pdb=" O THR A 324 " 0.021 2.00e-02 2.50e+03 pdb=" N CYS A 325 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN S 13 " 0.050 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO S 14 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO S 14 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO S 14 " 0.041 5.00e-02 4.00e+02 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1199 2.75 - 3.29: 8068 3.29 - 3.83: 13913 3.83 - 4.36: 16869 4.36 - 4.90: 30336 Nonbonded interactions: 70385 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.217 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.233 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 176 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.252 3.040 ... (remaining 70380 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.190 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 8839 Z= 0.226 Angle : 0.732 12.295 11994 Z= 0.427 Chirality : 0.053 0.856 1400 Planarity : 0.005 0.078 1508 Dihedral : 12.922 84.108 3088 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.69 % Favored : 96.13 % Rotamer: Outliers : 0.22 % Allowed : 0.88 % Favored : 98.90 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.25), residues: 1112 helix: 0.33 (0.28), residues: 370 sheet: -0.43 (0.31), residues: 276 loop : -1.68 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 161 TYR 0.024 0.001 TYR S 176 PHE 0.022 0.002 PHE R 25 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 8838) covalent geometry : angle 0.73164 (11992) SS BOND : bond 0.00768 ( 1) SS BOND : angle 1.58525 ( 2) hydrogen bonds : bond 0.14139 ( 419) hydrogen bonds : angle 5.94993 ( 1191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.326 Fit side-chains REVERT: A 28 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7674 (mt-10) REVERT: B 134 ARG cc_start: 0.8079 (ptt90) cc_final: 0.7575 (ptt-90) REVERT: B 221 THR cc_start: 0.8845 (t) cc_final: 0.8308 (m) outliers start: 2 outliers final: 0 residues processed: 133 average time/residue: 0.0935 time to fit residues: 16.6843 Evaluate side-chains 118 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 30.0000 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 215 ASN A 306 GLN B 17 GLN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.158748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.118675 restraints weight = 9337.427| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.62 r_work: 0.2811 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 8839 Z= 0.268 Angle : 0.680 8.433 11994 Z= 0.362 Chirality : 0.047 0.242 1400 Planarity : 0.005 0.069 1508 Dihedral : 5.889 69.816 1227 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.05 % Favored : 95.77 % Rotamer: Outliers : 1.43 % Allowed : 7.46 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.24), residues: 1112 helix: 0.41 (0.27), residues: 374 sheet: -0.31 (0.29), residues: 278 loop : -1.69 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 72 TYR 0.019 0.002 TYR S 176 PHE 0.017 0.002 PHE R 25 TRP 0.020 0.002 TRP B 82 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00653 ( 8838) covalent geometry : angle 0.67997 (11992) SS BOND : bond 0.00793 ( 1) SS BOND : angle 1.90339 ( 2) hydrogen bonds : bond 0.05495 ( 419) hydrogen bonds : angle 4.98187 ( 1191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.243 Fit side-chains REVERT: A 28 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7993 (mt-10) REVERT: A 186 GLU cc_start: 0.7896 (tt0) cc_final: 0.7678 (tt0) REVERT: A 197 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8080 (mmtt) REVERT: B 217 MET cc_start: 0.8400 (ppp) cc_final: 0.8088 (ppp) outliers start: 13 outliers final: 10 residues processed: 126 average time/residue: 0.1103 time to fit residues: 18.6122 Evaluate side-chains 125 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.0970 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 0.0170 chunk 8 optimal weight: 0.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.169921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129815 restraints weight = 9297.412| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.08 r_work: 0.3029 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8839 Z= 0.113 Angle : 0.523 7.801 11994 Z= 0.281 Chirality : 0.042 0.223 1400 Planarity : 0.004 0.058 1508 Dihedral : 5.334 69.931 1227 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.97 % Favored : 96.85 % Rotamer: Outliers : 1.54 % Allowed : 10.53 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.25), residues: 1112 helix: 0.95 (0.28), residues: 376 sheet: -0.11 (0.29), residues: 277 loop : -1.58 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 87 TYR 0.013 0.001 TYR S 191 PHE 0.011 0.001 PHE B 151 TRP 0.011 0.001 TRP R 207 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8838) covalent geometry : angle 0.52302 (11992) SS BOND : bond 0.00490 ( 1) SS BOND : angle 0.96998 ( 2) hydrogen bonds : bond 0.03874 ( 419) hydrogen bonds : angle 4.52010 ( 1191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.343 Fit side-chains REVERT: A 28 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7956 (mt-10) REVERT: B 217 MET cc_start: 0.8281 (ppp) cc_final: 0.7860 (ptm) REVERT: S 82 GLN cc_start: 0.7772 (tp40) cc_final: 0.6398 (mp10) outliers start: 14 outliers final: 9 residues processed: 131 average time/residue: 0.1186 time to fit residues: 20.5555 Evaluate side-chains 122 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.159018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.117836 restraints weight = 9382.740| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.66 r_work: 0.2849 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8839 Z= 0.251 Angle : 0.628 7.726 11994 Z= 0.335 Chirality : 0.046 0.223 1400 Planarity : 0.005 0.066 1508 Dihedral : 5.624 70.136 1227 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.41 % Favored : 95.41 % Rotamer: Outliers : 2.19 % Allowed : 12.17 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.24), residues: 1112 helix: 0.73 (0.27), residues: 377 sheet: -0.16 (0.29), residues: 283 loop : -1.55 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 68 TYR 0.011 0.002 TYR B 85 PHE 0.018 0.002 PHE R 25 TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00611 ( 8838) covalent geometry : angle 0.62772 (11992) SS BOND : bond 0.00680 ( 1) SS BOND : angle 1.96897 ( 2) hydrogen bonds : bond 0.05015 ( 419) hydrogen bonds : angle 4.64457 ( 1191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.337 Fit side-chains REVERT: A 28 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7986 (mt-10) REVERT: A 197 LYS cc_start: 0.8518 (mttm) cc_final: 0.8182 (mttp) REVERT: A 318 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7629 (mt-10) REVERT: B 217 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7958 (ptm) REVERT: S 82 GLN cc_start: 0.7789 (tp40) cc_final: 0.6340 (mp10) outliers start: 20 outliers final: 15 residues processed: 130 average time/residue: 0.1046 time to fit residues: 18.0803 Evaluate side-chains 132 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 113 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 107 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 108 optimal weight: 20.0000 chunk 35 optimal weight: 0.0000 chunk 74 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.170278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130652 restraints weight = 9420.533| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.74 r_work: 0.3040 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8839 Z= 0.106 Angle : 0.505 6.897 11994 Z= 0.271 Chirality : 0.041 0.235 1400 Planarity : 0.004 0.057 1508 Dihedral : 5.237 69.946 1227 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.15 % Favored : 96.76 % Rotamer: Outliers : 1.97 % Allowed : 13.05 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.25), residues: 1112 helix: 1.25 (0.27), residues: 376 sheet: -0.01 (0.29), residues: 285 loop : -1.39 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 68 TYR 0.012 0.001 TYR S 191 PHE 0.021 0.001 PHE R 25 TRP 0.011 0.001 TRP R 207 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8838) covalent geometry : angle 0.50517 (11992) SS BOND : bond 0.00410 ( 1) SS BOND : angle 0.87065 ( 2) hydrogen bonds : bond 0.03638 ( 419) hydrogen bonds : angle 4.33944 ( 1191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8147 (mt-10) REVERT: A 197 LYS cc_start: 0.8452 (mttm) cc_final: 0.8154 (mttp) REVERT: A 309 ASP cc_start: 0.7874 (m-30) cc_final: 0.7672 (m-30) REVERT: A 318 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7638 (mt-10) REVERT: S 82 GLN cc_start: 0.7859 (tp40) cc_final: 0.6562 (mp10) outliers start: 18 outliers final: 13 residues processed: 126 average time/residue: 0.1220 time to fit residues: 20.4332 Evaluate side-chains 127 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 239 LYS Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 83 optimal weight: 20.0000 chunk 92 optimal weight: 0.0770 chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.171396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.131908 restraints weight = 9372.956| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.58 r_work: 0.3078 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8839 Z= 0.102 Angle : 0.485 5.852 11994 Z= 0.260 Chirality : 0.041 0.249 1400 Planarity : 0.004 0.052 1508 Dihedral : 5.025 70.414 1227 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.52 % Allowed : 13.49 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.25), residues: 1112 helix: 1.46 (0.28), residues: 379 sheet: 0.08 (0.29), residues: 292 loop : -1.25 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 68 TYR 0.012 0.001 TYR S 191 PHE 0.012 0.001 PHE R 51 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 8838) covalent geometry : angle 0.48447 (11992) SS BOND : bond 0.00412 ( 1) SS BOND : angle 0.88370 ( 2) hydrogen bonds : bond 0.03378 ( 419) hydrogen bonds : angle 4.17313 ( 1191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8015 (mt-10) REVERT: B 221 THR cc_start: 0.8977 (t) cc_final: 0.8322 (m) REVERT: S 82 GLN cc_start: 0.7818 (tp40) cc_final: 0.6581 (mp10) outliers start: 23 outliers final: 12 residues processed: 133 average time/residue: 0.1199 time to fit residues: 21.0899 Evaluate side-chains 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 0.0970 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 0.0570 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.173069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132995 restraints weight = 9399.589| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.64 r_work: 0.3081 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8839 Z= 0.094 Angle : 0.472 6.143 11994 Z= 0.254 Chirality : 0.041 0.256 1400 Planarity : 0.004 0.051 1508 Dihedral : 4.888 70.932 1227 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.86 % Allowed : 13.82 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.25), residues: 1112 helix: 1.71 (0.28), residues: 377 sheet: 0.17 (0.29), residues: 292 loop : -1.12 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 68 TYR 0.012 0.001 TYR S 191 PHE 0.022 0.001 PHE R 25 TRP 0.008 0.001 TRP B 82 HIS 0.002 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 8838) covalent geometry : angle 0.47164 (11992) SS BOND : bond 0.00381 ( 1) SS BOND : angle 0.81333 ( 2) hydrogen bonds : bond 0.03175 ( 419) hydrogen bonds : angle 4.07568 ( 1191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7452 (mtp180) cc_final: 0.7145 (ttp-110) REVERT: A 28 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8005 (mt-10) REVERT: B 221 THR cc_start: 0.8946 (t) cc_final: 0.8268 (m) REVERT: B 258 ASP cc_start: 0.6845 (t70) cc_final: 0.6572 (t70) REVERT: S 82 GLN cc_start: 0.7908 (tp40) cc_final: 0.6547 (mp10) outliers start: 17 outliers final: 13 residues processed: 129 average time/residue: 0.1158 time to fit residues: 19.8442 Evaluate side-chains 127 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 MET Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 1 optimal weight: 30.0000 chunk 108 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.166881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.126379 restraints weight = 9393.856| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.83 r_work: 0.2979 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8839 Z= 0.193 Angle : 0.565 6.606 11994 Z= 0.303 Chirality : 0.044 0.271 1400 Planarity : 0.004 0.058 1508 Dihedral : 5.270 71.750 1227 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.86 % Allowed : 15.35 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.25), residues: 1112 helix: 1.42 (0.27), residues: 378 sheet: 0.19 (0.29), residues: 289 loop : -1.28 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 68 TYR 0.010 0.002 TYR S 59 PHE 0.014 0.002 PHE S 29 TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 8838) covalent geometry : angle 0.56487 (11992) SS BOND : bond 0.00572 ( 1) SS BOND : angle 1.61403 ( 2) hydrogen bonds : bond 0.04331 ( 419) hydrogen bonds : angle 4.33815 ( 1191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8087 (mt-10) REVERT: A 351 CYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6794 (p) REVERT: B 258 ASP cc_start: 0.6959 (t70) cc_final: 0.6682 (t70) REVERT: S 82 GLN cc_start: 0.7895 (tp40) cc_final: 0.6439 (mp10) outliers start: 17 outliers final: 13 residues processed: 126 average time/residue: 0.1069 time to fit residues: 18.1320 Evaluate side-chains 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.171280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.130344 restraints weight = 9349.468| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.96 r_work: 0.3058 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8839 Z= 0.111 Angle : 0.498 6.805 11994 Z= 0.268 Chirality : 0.041 0.273 1400 Planarity : 0.004 0.054 1508 Dihedral : 5.051 72.404 1227 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.75 % Allowed : 15.79 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.25), residues: 1112 helix: 1.60 (0.27), residues: 379 sheet: 0.22 (0.29), residues: 291 loop : -1.16 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 68 TYR 0.011 0.001 TYR S 191 PHE 0.011 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8838) covalent geometry : angle 0.49830 (11992) SS BOND : bond 0.00414 ( 1) SS BOND : angle 1.01104 ( 2) hydrogen bonds : bond 0.03497 ( 419) hydrogen bonds : angle 4.22365 ( 1191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8052 (mt-10) REVERT: A 277 LYS cc_start: 0.7743 (mtpp) cc_final: 0.7124 (mttp) REVERT: A 351 CYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6736 (p) REVERT: B 221 THR cc_start: 0.8948 (t) cc_final: 0.8300 (m) REVERT: B 258 ASP cc_start: 0.6876 (t70) cc_final: 0.6593 (t70) REVERT: S 82 GLN cc_start: 0.7801 (tp40) cc_final: 0.6377 (mp10) outliers start: 16 outliers final: 13 residues processed: 125 average time/residue: 0.1038 time to fit residues: 17.2017 Evaluate side-chains 127 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 7 optimal weight: 0.0050 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 0.0070 chunk 12 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 overall best weight: 0.5614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.173004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.132662 restraints weight = 9335.108| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.66 r_work: 0.3188 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8839 Z= 0.096 Angle : 0.480 7.088 11994 Z= 0.257 Chirality : 0.041 0.255 1400 Planarity : 0.004 0.051 1508 Dihedral : 4.911 73.273 1227 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.43 % Allowed : 16.34 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.26), residues: 1112 helix: 1.81 (0.28), residues: 378 sheet: 0.27 (0.29), residues: 292 loop : -1.09 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 68 TYR 0.011 0.001 TYR S 191 PHE 0.010 0.001 PHE B 151 TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 8838) covalent geometry : angle 0.47966 (11992) SS BOND : bond 0.00399 ( 1) SS BOND : angle 0.88823 ( 2) hydrogen bonds : bond 0.03192 ( 419) hydrogen bonds : angle 4.10650 ( 1191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7462 (mtp180) cc_final: 0.7180 (ttp-110) REVERT: A 28 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8028 (mt-10) REVERT: A 273 LEU cc_start: 0.8111 (mp) cc_final: 0.7829 (mp) REVERT: A 277 LYS cc_start: 0.7728 (mtpp) cc_final: 0.7133 (mttp) REVERT: B 221 THR cc_start: 0.8944 (t) cc_final: 0.8282 (m) REVERT: B 258 ASP cc_start: 0.6892 (t70) cc_final: 0.6654 (t70) REVERT: S 82 GLN cc_start: 0.7875 (tp40) cc_final: 0.6607 (mp10) outliers start: 13 outliers final: 13 residues processed: 127 average time/residue: 0.1117 time to fit residues: 18.7669 Evaluate side-chains 128 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.173239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134148 restraints weight = 9256.288| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.51 r_work: 0.3054 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8839 Z= 0.121 Angle : 0.501 6.937 11994 Z= 0.269 Chirality : 0.042 0.223 1400 Planarity : 0.004 0.052 1508 Dihedral : 4.989 73.635 1227 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.86 % Allowed : 16.12 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.25), residues: 1112 helix: 1.79 (0.27), residues: 377 sheet: 0.26 (0.29), residues: 292 loop : -1.11 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 68 TYR 0.011 0.001 TYR S 191 PHE 0.011 0.001 PHE B 151 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8838) covalent geometry : angle 0.50123 (11992) SS BOND : bond 0.00464 ( 1) SS BOND : angle 1.09684 ( 2) hydrogen bonds : bond 0.03519 ( 419) hydrogen bonds : angle 4.19100 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2166.65 seconds wall clock time: 37 minutes 51.44 seconds (2271.44 seconds total)